Différenciation des bactéroïdes chez les Aeschynomene

The ability of legumes to acquire sufficient nitrogen from the symbiosis with Rhizobium relies on the intimate contact between the endosymbiotic, intracellular rhizobia, called bacteroids, and their host cells, the symbiotic nodule cells. A well-studied example is the symbiotic nitrogen fixing bacterium Sinorhizobium meliloti, which nodulates the legume Medicago truncatula. Nodules of M. truncatula produce an enormous diversity of peptides called NCRs which are similar to antimicrobial peptides (AMPs) of innate immune systems. These NCRs are involved in maintaining the homeostasis between the host cells in the nodules and the large bacterial population they contain. Although many NCRs are genuine AMPs which kill microbes in vitro, in nodule cells they do not kill the bacteria but induce them into the terminally differentiated bacteroid state involving cell elongation, genome amplification, membrane fragilization and loss of cell division capacity. Protection against the antimicrobial action of NCRs by the bacterial BacA protein is critical for bacteroid survival in the symbiotic cells and thus for symbiosis. As a part of my PhD thesis, I have shown that the differentiation of the symbiotic cells in M. truncatula is associated with a tremendous transcriptional reprogramming involving hundreds of genes, mainly NCR genes, which are only expressed in these cells. Although the extensive work on the model M. truncatula/S. meliloti, little is known how the plant controls its intracellular population and imposes its differentiation into a functional form, the bacteroids in other symbiotic systems.In my PhD work, I provide several independent pieces of evidence to show that tropical legumes of the Aeschynomene genus which belong to the Dalbergoid legume clade use a different class of cysteine rich peptides (NCR-like) to govern bacteroid differentiation. This mechanism is similar to the one previously described in Medicago which was up to now assumed to be restricted to the advanced IRLC legume clade, to which it belongs. I have also shown that the Bradyrhizobium symbionts of Aeschynomene legumes possess a multidrug transporter, named BclA, which mediates the import of a diversity of peptides including NCR peptides. In the absence of this transporter, the rhizobia do not differentiate and do not fix nitrogen. BclA has a transmembrane domain of the same family as the transmembrane domain of the BacA transporter of Rhizobium and Sinorhizobium species which is known to be required in these rhizobia to respond to the NCR peptides of IRLC legumes. Again this is a mechanism which is analogous to the one described in S. meliloti the symbiont of Medicago.This study broaden our knowledge on the evolution of symbiosis by showing that the modus operandi involving peptides derived from innate immunity used by some legumes to keep their intracellular bacterial population under control is more widespread and ancient than previously thought and has been invented by evolution several times.Les Légumineuses ont développé une interaction symbiotique avec des bactéries du sol, les rhizobia, qui fixent l’azote atmosphérique et le transfèrent à la plante sous forme assimilable.Cette interaction a lieu, au sein des nodosités, des organes racinaires où les bactéries intracellulaires se différencient en bactéroïdes. Chez Medicago truncatula, ces bactéroïdes correspondent à un stade de différentiation terminale corrélée à une endoréplication de leur génome, une augmentation de la taille des cellules, une modification des membranes et une faible capacité à se propager. Cette différentiation est induite par des facteurs de la plante appelés NCR (Nodule-specific Cysteine Rich). Les peptides NCRs ressemblent à des défensines, des peptides antimicrobiens ayant une activité antimicrobienne in vitro, tuant des bactéries. Ainsi, un élément clef dans la différenciation des bactéroïdes est la protéine bactérienne BacA, un transporteur membranaire qui confère une résistance contre l’activité antimicrobienne des peptides. Dans le cadre de ce travail de thèse, j’ai montré que l'expression des NCR est soumise à une régulation stricte et qu’ils sont activés dans trois vagues dans les cellules symbiotiques polyploïdes.Les mécanismes de contrôle par la plante sur les rhizobia intracellulaires demeurent à ce jourpeu connus et le seul modèle étudié, au début de ce travail de thèse, restait l'interaction entre M. truncatula et S. meliloti. Je me suis donc intéressée à la symbiose de certaines Légumineuses tropicales du genre Aeschynomene appartenant au clade des Dalbergoïdes où jemontre qu’ils utilisent une classe différente de peptides riches en cystéine (NCR-like) pour induire la différenciation des bactéroïdes. Ce mécanisme est analogue à celui décrit précédemment chez Medicago qui était jusqu'à présent supposé être limitée aux légumineuses appartenant au clade des IRLC. J’ai également montré que Bradyrhizobium, symbionte d’Aeschynomene possèdent un transporteur de type ABC homologues à BacA de Sinorhizobium nommé BclA. Ce gène permet l'importation d'une variété de peptides comprenant des peptides NCR. En l'absence de ce transporteur, les rhizobiums sont incapables de se différencier et de fixer l'azote.Cette étude a permis d'élargir nos connaissances sur l'évolution de la symbiose en montrant qu’au cours de l’évolution, deux clades de Légumineuses relativement éloignés (IRLC et Dalbergoïdes) aient convergé vers l’utilisation de peptides de l’immunité innée afin de contrôler leur symbionte bactérien et d’en tirer un bénéfice maximal au cours de l’interaction symbiotique

From Intracellular Bacteria to Differentiated Bacteroids: Transcriptome and Metabolome Analysis in Aeschynomene Nodules Using the Bradyrhizobium sp. Strain ORS285 bclA Mutant

Soil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells, where they differentiate into nitrogen-fixing bacteroids. Several legume lineages force their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. strain ORS285, a symbiont of Aeschynomene spp. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells, but they cannot differentiate into enlarged polyploid and functional bacteroids. Thus, the bclA nodule bacteria constitute an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied by a first transcriptome switch involving several hundred upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving fewer genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a nonsymbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids. IMPORTANCE Legume-rhizobium symbiosis is a major ecological process, fueling the biogeochemical nitrogen cycle with reduced nitrogen. It also represents a promising strategy to reduce the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs, where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle

Bradyrhizobium BclA is a peptide transporter required for bacterial differentiation in symbiosis with Aeschynomene legumes.

Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called NCRs in the symbiotic nodule cells which house the bacteroids. NCRs are related to antimicrobial peptides of innate immunity. They induce the endosymbionts into a differentiated, enlarged and polyploid state. The bacterial symbionts on their side evolved functions for the response to the NCR peptides. Here we identified the bclA gene of Bradyrhizobium strains ORS278 and ORS285 which is required for the formation of differentiated and functional bacteroids in the nodules of the NCR-producing Aeschynomene legumes. The BclA ABC transporter promotes the import of NCR peptides and provides protection against the antimicrobial activity of these peptides. Moreover, BclA can complement the role of the related BacA transporter of Sinorhizobium meliloti which has a similar symbiotic function in the interaction with Medicago legumes

Extreme specificity of NCR gene expression in Medicago truncatula

Background: Legumes form root nodules to house nitrogen fixing bacteria of the rhizobium family. The rhizobia are located intracellularly in the symbiotic nodule cells. In the legume Medicago truncatula these cells produce high amounts of Nodule-specific Cysteine-Rich (NCR) peptides which induce differentiation of the rhizobia into enlarged, polyploid and non-cultivable bacterial cells. NCRs are similar to innate immunity antimicrobial peptides. The NCR gene family is extremely large in Medicago with about 600 genes. Results: Here we used the Medicago truncatula Gene Expression Atlas (MtGEA) and other published microarray data to analyze the expression of 334 NCR genes in 267 different experimental conditions. We find that all but five of these genes are expressed in nodules but in no other plant organ or in response to any other biotic interaction or abiotic stress tested. During symbiosis, none of the genes are induced by Nod factors. The NCR genes are activated in successive waves during nodule organogenesis, correlated with bacterial infection of the nodule cells and with a specific spatial localization of their transcripts from the apical to the proximal nodule zones. However, NCR expression is not associated with nodule senescence. According to their Shannon entropy, a measure expressing tissue specificity of gene expression, the NCR genes are among the most specifically expressed genes in M. truncatula. Moreover, when activated in nodules, their expression level is among the highest of all genes. Conclusions: Together, these data show that the NCR gene expression is subject to an extreme tight regulation and is only activated during nodule organogenesis in the polyploid symbiotic cells

Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules

International audienceLegumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway

A nonRD receptor-like kinase prevents nodule early senescence and defense-like reactions during symbiosis

International audienceRhizobia and legumes establish symbiotic interactions leading to the production of root nodules, in which bacteria fix atmospheric nitrogen for the plant's benefit. This symbiosis is efficient because of the high rhizobia population within nodules. Here, we investigated how legumes accommodate such bacterial colonization. We used a reverse genetic approach to identify a Medicago truncatula gene, SymCRK, which encodes a cysteine-rich receptor-like kinase that is required for rhizobia maintenance within the plant cells, and performed detailed phenotypic analyses of the corresponding mutant. The Medicago truncatula symCRK mutant developed nonfunctional and necrotic nodules. A nonarginine asparate (nonRD) motif, typical of receptors involved in innate immunity, is present in the SymCRK kinase domain. Similar to the dnf2 mutant, bacteroid differentiation defect, defense-like reactions and early senescence were observed in the symCRK nodules. However, the dnf2 and symCRK nodules differ by their degree of colonization, which is higher in symCRK. Furthermore, in contrast to dnf2, symCRK is not a conditional mutant. These results suggest that in M. truncatula at least two genes are involved in the symbiotic control of immunity. Furthermore, phenotype differences between the two mutants suggest that two distinct molecular mechanisms control suppression of plant immunity during nodulation

Specific Host-Responsive Associations Between Medicago truncatula Accessions and Sinorhizobium Strains

Legume plants interact with rhizobia to form nitrogen-fixing root nodules. Legume-rhizobium interactions are specific and only compatible rhizobia and plant species will lead to nodule formation. Even within compatible interactions, the genotype of both the plant and the bacterial symbiont will impact on the efficiency of nodule functioning and nitrogen-fixation activity. The model legume Medicago truncatula forms nodules with several species of the Sinorhizobium genus. However, the efficiency of these bacterial strains is highly variable. In this study, we compared the symbiotic efficiency of Sinorhizobium meliloti strains Sm1021, 102F34, and FSM-MA, and Sinorhizobium medicae strain WSM419 on the two widely used M. truncatula accessions A17 and R108. The efficiency of the interactions was determined by multiple parameters. We found a high effectiveness of the FSM-MA strain with both M. truncatula accessions. In contrast, specific highly efficient interactions were obtained for the A17-WSM419 and R108-102F34 combinations. Remarkably, the widely used Sm1021 strain performed weakly on both hosts. We showed that Sm1021 efficiently induced nodule organogenesis but cannot fully activate the differentiation of the symbiotic nodule cells, explaining its weaker performance. These results will be informative for the selection of appropriate rhizobium strains in functional studies on symbiosis using these M. truncatula accessions, particularly for research focusing on late stages of the nodulation process

From intracellular bacteria to differentiated bacteroids: transcriptome and metabolome analysis in Aeschynomene nodules using the Bradyrhizobium sp. ORS285 bclA mutant

International audienceSoil bacteria called rhizobia trigger the formation of root nodules on legume plants. The rhizobia infect these symbiotic organs and adopt an intracellular lifestyle within the nodule cells where they differentiate into nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, the bacteria proceed until the intracellular infection of nodule cells but they cannot differentiate into enlarged polyploid and functional bacteroids. The bclA nodule bacteria constitute thus an intermediate stage between the free-living soil bacteria and the nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but ones that are expressed to extremely elevated levels. The transcriptomes further suggested a dynamic role for oxygen and redox regulation of gene expression during nodule formation and a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.ImportanceThe legume-rhizobium symbiosis is a major ecological process fueling the biogeochemical nitrogen cycle with reduced nitrogen. It represents also a promising strategy to cut down the use of chemical nitrogen fertilizers in agriculture, thereby improving its sustainability. This interaction leads to the intracellular accommodation of rhizobia within plant cells of symbiotic organs where they differentiate into nitrogen-fixing bacteroids. In specific legume clades, this differentiation process requires the bacterial transporter BclA to counteract antimicrobial peptides produced by the host. Transcriptome analysis of Bradyrhizobium wild-type and bclA mutant bacteria in culture and in symbiosis with Aeschynomene host plants dissected the bacterial transcriptional response in distinct phases and highlighted functions of the transporter in the free-living stage of the bacterial life cycle

Sinorhizobium fredii HH103 bacteroids are not terminally differentiated and show altered O-antigen in nodules of the Inverted Repeat-Lacking Clade legume Glycyrrhiza uralensis.

International audienceIn rhizobial species that nodulate inverted repeat-lacking clade (IRLC) legumes, such as the interaction between Sinorhizobium meliloti and Medicago, bacteroid differentiation is driven by an endoreduplication event that is induced by host nodule-specific cysteine rich (NCR) antimicrobial peptides and requires the participation of the bacterial protein BacA. We have studied bacteroid differentiation of Sinorhizobium fredii HH103 in three host plants: Glycine max, Cajanus cajan and the IRLC legume Glycyrrhiza uralensis. Flow cytometry, microscopy analyses and viability studies of bacteroids as well as confocal microscopy studies carried out in nodules showed that S. fredii HH103 bacteroids, regardless of the host plant, had deoxyribonucleic acid (DNA) contents, cellular sizes and survival rates similar to those of free-living bacteria. Contrary to S. meliloti, S. fredii HH103 showed little or no sensitivity to Medicago NCR247 and NCR335 peptides. Inactivation of S. fredii HH103 bacA neither affected symbiosis with Glycyrrhiza nor increased bacterial sensitivity to Medicago NCRs. Finally, HH103 bacteroids isolated from Glycyrrhiza, but not those isolated from Cajanus or Glycine, showed an altered lipopolysaccharide. Our studies indicate that, in contrast to the S. meliloti-Medicago model symbiosis, bacteroids in the S. fredii HH103-Glycyrrhiza symbiosis do not undergo NCR-induced and bacA-dependent terminal differentiation